Step 1
Place racks in upper and lower thirds of oven; preheat to 350°. Scatter 1 cup coarsely chopped raw pecans on a rimmed baking sheet and 1 cup (packed) unsweetened coconut flakes on another rimmed baking sheet. Toast coconuts and pecans, rotating baking sheets top to bottom and front to back and stirring after 5 minutes, until nuts are slightly darkened in color and fragrant and coconut is golden, 6–8 minutes for nuts and 5–7 minutes for coconut. (They will not be done at the same time.) Let cool on baking sheets; turn off oven.
Step 2
Toss remaining ¾ cup coarsely chopped raw pecans and remaining ¾ cup (packed) unsweetened coconut flakes in a medium bowl to combine; set aside.
Step 3
Beat 1 cup (2 sticks) unsalted butter, room temperature, 1 cup (packed; 200 g) dark brown sugar, and ½ cup (100 g) granulated sugar in the bowl of a stand mixer fitted with the paddle attachment on medium-high speed, scraping down sides of bowl as needed, until light and fluffy, about 2 minutes. Add 2 large eggs, room temperature, 2 Tbsp. pure maple syrup, and 1 Tbsp. vanilla extract, and beat until pale and very fluffy, about 2 minutes. Add 1¾ cups (219 g) all-purpose flour, 2½ tsp. Diamond Crystal or 1½ tsp. Morton kosher salt, 1 tsp. baking soda, and 1 tsp. ground cinnamon and mix just until no pockets of dry flour remain, about 1 minute. Remove bowl from stand mixer and add toasted pecans, toasted coconut, 8 oz. semisweet chocolate, chopped, and 3 cups old-fashioned oats; stir with a rubber spatula just until evenly distributed.
Step 4
Using a #16 cookie scoop or ¼-cup measure and working one at a time, portion out dough and roll in reserved mixed raw coconut and pecans, shaping into balls to help pecan mixture stick to the outside, until evenly coated. Place balls on a parchment-lined baking sheet and chill, uncovered, at least 45 minutes.
Step 5
Preheat oven to 350° (leave racks in upper and lower thirds of oven). Place 8 chilled dough balls on each of 2 fresh parchment-lined baking sheets, spacing about 2″ apart. Bake cookies, rotating baking sheets top to bottom and front to back halfway through, until golden brown around the edges and puffed slightly (they should still be slightly wet-looking in the cracks), 17–19 minutes. (If cookies are too puffed, press down lightly on the tops as soon as they come out of the oven.) Let cookies cool on baking sheets and sprinkle with flaky sea salt, if using. Repeat with remaining baking sheet of cookies. (If you need to reuse a baking sheet, let cool at least 15 minutes before baking on it again.)
Do Ahead: Dough can be formed into balls 12 hours ahead; cover and keep chilled. Cookies can be baked 3 days ahead; store airtight at room temperature.